dREG

dREG identifies regulatory DNA sequences from nascent RNA sequencing data (GRO-seq) to locate functional genomic regions in mammalian genomes.

Key Features:

• GRO-seq support: Processes nascent RNA sequencing data from Global Run-On Sequencing (GRO-seq) to detect regulatory elements.
• dREG algorithm: Implements the dREG algorithm for online computation of functional genomic regions using GRO-seq signals.
• R package: Provides an R package implementing dREG functionality.
• XSEDE integration: Leverages the Extreme Science and Engineering Discovery Environment (XSEDE) for CPUs, GPUs, and storage in large-scale analyses.
• Airavata/PGA integration: Integrates the PHP Gateway for Airavata (PGA) and Apache Airavata frameworks to interface with HPC resources.
• GPU acceleration: Supports GPU computing resources for computationally demanding analyses.

Scientific Applications:

• Regulatory element identification: Identifies regulatory DNA sequences and functional genomic regions from GRO-seq data.
• Gene regulation mapping: Maps genomic regions implicated in gene expression regulation in mammalian genomes.
• Nascent transcription analysis: Enables large-scale analysis of nascent transcription using GRO-seq.

Methodology:

dREG applies the dREG algorithm for online computation of functional genomic regions from GRO-seq data and interfaces with XSEDE HPC resources via the PHP Gateway for Airavata (PGA) and Apache Airavata, with support for CPU and GPU resources.